Drew and L'Etoile were definitely significant losses for the game, Drew for the general world-building for the various species and for the Citadel races, making an emphasis on how humanity wasn't the driving force for civilization as we know it, and L'Etoile for defying conventions with the characters under his care - Thane and Legion are both extremely alien in their attitudes, not just human-like, just with bumpy foreheads, which made them much more difficult to write for. That's the big flaw of the Rannoch arc, that Legion and the geth stop being the same geth from ME2 and become 'traditional' AIs, looking to be more 'human,' when in ME2, Legion was openly critical of the independence favored by organics. It's not that it's not a story worth telling, or a bad story to begin with, just that it doesn't follow from where the story began. So once those two were gone, gone two thirds of the way into a trilogy, everyone else had to somewhat scramble to fill in the gaps as best as they could however they could. It's understandable, it just leaves a few significant gaps in the course of the characters and the storylines.
On the original topic, I tend to take the games as 'primary canon,' as that's where the series originates, and everything else is broader, more 'this is roughly what happened, but it may not have gone exactly like this.' There are points where the movie, the novels, and the comics diverge from what's established in the games, so in those cases, games trump comics (so the last five minutes-ish of Paragon Lost didn't really happen since James says he got his recommendation for the N7 program on the day the Reapers hit Earth in the game, Kaidan's telling of things at Brain Camp to Shepard isn't in line with the comic so I go with the game's explanation... etc.) and otherwise, I try not to think about it. The thing with multimedia franchises is how easily the 'canon' can spiral out of hand.
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